Solution
For any addon devs: CTMod 8.3.0.10 fixed this using the following code:
CinematicFrame:SetScript("OnShow", nil)
CinematicFrame:SetScript("OnHide", nil)
Fundamentally, the problem was that WorldFrame was being altered by the OnShow/OnHide scripts during combat, but then the addon couldn't override and put it back to the custom settings afterwards because of combat lockdown.
As far as I know, this is only an issue with fights like Jaina and Mythic N'Zoth.
My thanks to G1ak1 for finding me on Curse and reporting the issue so I could fix it.
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